Persistence Length of Chromatin Determines Origin Spacing in Xenopus Early-Embryo DNA Replication: Quantitative Comparisons between Theory and Experiment

Abstract

In Xenopus early embryos, replication origins neither require specific DNA sequences nor is there an efficient S/M checkpoint, even though the whole genome (3 billion bases) is completely duplicated within 10-20 minutes. This leads to the "random-completion problem" of DNA replication in embryos, where one needs to find a mechanism that ensures complete, faithful, timely reproduction of the genome without any sequence dependence of replication origins. We analyze recent DNA replication data in Xenopus laevis egg extracts and find discrepancies with models where replication origins are distributed independently of chromatin structure. Motivated by these discrepancies, we have investigated the role that chromatin looping may play in DNA replication. We find that the loop-size distribution predicted from a wormlike-chain model of chromatin can account for the spatial distribution of replication origins in this system quantitatively. Together with earlier findings of increasing frequency of origin firings, our results can explain the random-completion problem. The agreement between experimental data (molecular combing) and theoretical predictions suggests that the intrinsic stiffness of chromatin loops plays a fundamental biological role in DNA replication in early-embryo Xenopus in regulating the origin spacing.

DNA Replication Origins Fire Stochastically in Fission Yeast

“…The observation that origins do not fire in every cell cycle raises the question of how individual origins are selected to fire and if that selection is distributed in a coordinated manner. In the absence of such coordination, origin firing would be randomly distributed, leading to the random gap problem; some cells would have large gaps between origin firing that would take a long time to replicate (Lucas et al, 2000;Herrick et al, 2002;Hyrien et al, 2003;Jun et al, 2004). Simple models of replication kinetics predict that if replication origins are randomly distributed, ϳ5% of the cells will have such large gaps between active origins that they will take four times longer than average to replicate (see Materials and Methods for calculations).…”

DNA replication timing: random thoughts about origin firing

“…This 'increasing efficiency model' is particularly powerful because it is applicable to any eukaryotic genome or cell cycle, and, as discussed below, can accommodate different types of replication organization, from fast and heterogeneous in embryos, to slow and ordered in somatic cells. Furthermore, it can be modified to incorporate realistic descriptions of chromosome dynamics 26 . It should be noted that this model only addresses the random gaps caused by stochastic firing during S phase of established origins; it does not address the separate issue of how and where origins are established in G1.…”

Nucleation and growth in one dimension. I. The generalized Kolmogorov-Johnson-Mehl-Avrami model

“…We speculate that the same holds true for any local nucleation function I(x, t), a conclusion that is also supported by computer simulation [25,28]. Assuming a local nucleation function, we can write the formal expression for ρ i2i (x, t) directly in terms of ρ i (x, t) and ρ h (x, t): (19) where S designates the constraint plane shown in Fig.…”

“…For instance, whether homogeneous nucleation is a valid assumption cannot be known a priori. Indeed, in the recent DNA replication experiment that motivated this work, the "nucleation" sites for DNA replication along the genome were found to be not distributed randomly, a result that has important biological implications for cell-cycle regulation [25].…”